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Hi Pavel,
I am also trying to make kicked maps for the first time in order to improve
density for a terminal helix and short loop that have been giving me
problems in model building for an MR structure. On a similar note to Yarrow,
I tried using his syntax in a maps.params file, like this:
map {
mtz_label_amplitudes = 2FOFCWT_kick
mtz_label_phases = PH2FOFCWT_kick
likelihood_weighted = True
obs_factor = 2
calc_factor = 1
kicked = True
fill_missing_f_obs_with_weighted_f_model = False
}
map {
mtz_label_amplitudes = "FOFCWT_kicked"
mtz_label_phases = "PHFOFCWT_kicked"
likelihood_weighted = True
obs_factor = 1
calc_factor = 1
kicked = True
fill_missing_f_obs_with_weighted_f_model = False
}
But when I ran phenix.maps I received this message:
Unused parameter definitions:
maps.map.mtz_label_amplitudes (file "maps.params", line 29)
maps.map.mtz_label_phases (file "maps.params", line 30)
maps.map.likelihood_weighted (file "maps.params", line 31)
maps.map.obs_factor (file "maps.params", line 32)
maps.map.calc_factor (file "maps.params", line 33)
maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params",
line 35)
maps.map.mtz_label_amplitudes (file "maps.params", line 38)
maps.map.mtz_label_phases (file "maps.params", line 39)
maps.map.likelihood_weighted (file "maps.params", line 40)
maps.map.obs_factor (file "maps.params", line 41)
maps.map.calc_factor (file "maps.params", line 42)
maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params",
line 44)
*******************************************************************************
Sorry: Unused parameter definitions.
Next I tried using this in my .params file for phenix.refine:
refinement.electron_density_maps {
map {
map_type = "2mFo-DFc"
format = *xplor ccp4
file_name = None
kicked = True
fill_missing_f_obs = False
grid_resolution_factor = 0.25
scale = *sigma volume
region = *selection cell
atom_selection = None
atom_selection_buffer = 3
acentrics_scale = 2
centrics_pre_scale = 1
sharpening = False
sharpening_b_factor = None
}
map {
map_type = "mFo-DFc"
format = *xplor ccp4
file_name = None
kicked = True
fill_missing_f_obs = False
grid_resolution_factor = 0.25
scale = *sigma volume
region = *selection cell
atom_selection = None
atom_selection_buffer = 3
acentrics_scale = 2
centrics_pre_scale = 1
sharpening = False
sharpening_b_factor = None
}
When I opened the map_coeffs.mtz output file, it contains these columns
2FOFCWT_no_fill
PH2FOFCWT_no_fill
FOFCWT
PHFOFCWT
Are these the coefficients for the kicked maps?
Cheers,
Kyle
Kyle T. Dolan
Department of Biochemistry and Molecular Biology
The University of Chicago
[email protected]
On Mon, Aug 2, 2010 at 7:48 PM, Pavel Afonine
Hi Yarrow,
you can use GUI or the command line for doing this.
0) It would be best if you update to the latest version, although I believe it might work with the one you have too:
http://www.phenix-online.org/download/
1) GUI: launch PHENIX GUI and go to Maps -> Create Maps. then just add as many maps you want (or use pre-defined ones) and check a box for kick map.
2) From the command line type:
phenix.maps
and hit Enter (Return). That will create a file called something maps.params. Edit that file to add/remove the maps you need/ don't need and set
kicked = True
for the one you want to be "kicked", and then run
phenix.maps maps.params
Let me know if you have any questions or problems.
Good luck! Pavel.
On 8/2/10 5:38 PM, [email protected] wrote:
Hello,
Disclaimer: I am a newbie to both crystallagraphy and Phenix.
I am running phenix.refine (v1.6-289) in the command line
1. I want to make averaged "kicked-maps" but I keep getting a syntax error. I tried renaming "maps.param" but this file was not recognized.
2. When I enter Phenix.maps into the command line I get a message that syas "not implemented" I am trying to get the latest versiou of phenix installed.
The following is the syntax I put in my custom_params file Thanks
-Yarrow
refinement.main.number_of_macro_cycles = 2 #refinement.main.fix_rotamers = True refinement.refine.strategy = individual_sites+individual_adp refinement.output.prefix = CIN4_refine_omit refinement.output.serial = 12 refinement.output.write_def_file = True refinement.target_weights_wxc.scale = 0.2 refinement.main.max_number_of_interations=15
refinement.electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT_kicked" mtz_label_phases = "PHFOFCWT_kicked" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = false }
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